Neo Equestria Evangelion
by The Rei-Fan
Summary: In the year of Celestia's Reign Eleven Hundred and Fifteen the world nearly ended but for the efforts of a group of six little ponies. Twenty years later, the survivors have kept going but it seems that not all has been put to rest as they had hoped; the sacrifice had not brought them salvation, it had only held back that which was inevitable.
1. Chapter 1

**Neo-Equestria Evangelion**

**Chapter One:**

'As allies, we find ourselves, at the end of the world.'

_"When did you first realize that it was going to be different from all of the other times, that you were in trouble you might not get out of?"_

_"How did I know we were in trouble? Discord wasn't laughing anymore."_

* * *

Lightning and thunder flashed and crackled through the sky, arcing between unnatural black clouds and the Giant of Light. The Giant of Light, Adam: an otherworldly being, taller than a full grown dragon, bipedal but with proportions unknown to ponykind. The beast, if it could be called such, as it showed intelligence, was enraged, casting beams of energy from its form, cross shaped explosions burst forth from the ground wherever they struck.

Six ponies stood at the behemoth's feet, looking up at it in awe and fear, their bodies adorned with jeweled necklaces, with the exception of the one, a purple unicorn who wore a jeweled tiara. Beneath the fear and the shock was a grim determination; they would not leave without victory. There was too much at stake to fail, the entire world could end if this creature was allowed to run unchecked.

The noise, the...scream. Haunting, alien, it seemed to permeate the very _souls _of those who witnessed it, penetrate into the deepest layers of the mind, it felt wrong, angry. Agony. The giant's arm flew up and to the side, a blast issued forth from the palm of its appendage the beam of coherent energy lanced into a distortion in the air and dissipated in another cross shaped explosion.

"Can they really do it?" the draconequus asked, standing back from the brewing calamity, he was pouring everything he had into holding back the tide of destruction, keeping whatever was building from spreading to the rest of Equestria, the irony not lost on him.

"We must have hope, Discord. If you had told me a month ago that I would be standing beside you as an ally, I would have thought you mad. If anypony can do this, they can." The white alicorn replied, her own face hopeful as she watched the rainbow-hued energy beam of the Elements of Harmony streak towards the barely contained giant.

"I wouldn't need hope if I'd recognized this for what it was, anything that would have woken me up..." Discord tailed off, the rest not needing said, she would know what he meant. He watched with rising panic as the rainbow-energy enveloped the giant, it was... wrong. "It's not working..."

Discord watched in morbid fascination as the energy cone broke up, rebounded back into the six ponies that had created it. The impact knocked them apart like bowling pins: purple, cyan, white, orange, pink, yellow, all scattered by the blast.

Celestia took a few steps towards her ponies, her face twisting from her hopeful smile into rage, "If that doesn't work... I'll have to resort to-"

"No." Discord said, as he grabbed onto her with his right hand, "You can't. I'm changing the laws of physics around him to interfere with what he's doing and it's not even slowing him down. You don't stand a chance against that kind of power... You have to trust the ponies to figure it out... and it looks like they are."

Twilight was on her hooves again, the other five close behind, she was advancing, casting a spell into the element of magic, adding her own energy to this next attack, this last chance to stop the rampaging giant.

Celestia gasped as she read the runes hovering around her star pupil. "Discord, we have to stop her, she's putting too much of herself into that spell, it _will_kill her if she casts it."

It wasn't a complex spell, with that much power behind it there couldn't be much control. Twilight poured her essence into a wall of force that would blast its way through anything that tried to stop it, unmake it from existence. As she worked she was dimly aware of Celestia mouthing something, but it was far away, unimportant in the face of the task before her. Gathering the last fragments of her power, every last scrap of energy she could summon forth, she formed it into a torrent of raw magic and loosed it into the framework of the spell. There was a blinding light-

Celestia gritted her teeth as she frantically worked a counterspell, drawing on millenia of knowledge to safely disassemble the complex layers of runes constructed before her. Every second she could feel the surge of power building, could see Twilight weakening as she poured her very life into the spell. In a tremendous surge of will, she sent forth a dozen streams of magic, searching for Twilight's essence amongst the roiling waves of raw magical energy. There was a blinding light-

Discord watched the neat, precise march of runes, painful in their orderliness, studying the chaos that invaded them, the tiny infinitesimal flaws which would cause them to catastrophically crack and fail under the raw power of the spell within them. And then he reached out and did something so foreign, so utterly alien to his nature that he barely comprehended the concept of it. Smoothing the fabric of reality, he pulled the chaos away from the most dangerous failures, channeled it away harmlessly. Beneath his feet, tiles cracked and ruptured under the onslaught of raw chaos. There was a blinding light-

_Twenty years later..._  
_  
"All lines are currently busy, please hang up and try again later. All lines are curre-"_

The orange pegasus pressed her hoof onto the phone switch and disconnected the call. She'd been sent to New Canterlot by her mother and yet hadn't been told why. _'It's important... That's what matters.'_she thought to herself as she stood at the edge of the empty city.

Shops and vending stalls littered the roadsides, and not a pony in sight. It was as if everypony had simply walked away from what they were doing, meals were still on tables, coins still on counter-tops. Her only companion was the cadence in the distance. Tump-Tump. Tump-Thump.

_'Wait, what?'_ she thought in confusion, _'That wasn't there bef-'_"Oh my." she finished aloud. Standing over a hill just outside of town, just at the end of the road she was standing on, was a monster the likes of which she had never imagined.

Four hundred hooves tall, if not more, almost avian, almost draconic. It stood tall on two legs, with two spindly arms covered in boney plates coming from shoulders set far too broadly. The entire creature looked wrong, disproportionate and yet... terrifying. It's eyeless face covered in a mask of bone, a sharp beak adorned it, less the beak of a bird and more like a needle...

And it was staring directly at her.


	2. Chapter 2

**Neo-Equestria Evangelion**

**Chapter Two:**

'Rise, young foal, to the heavens, and become legend.'

_"I could have stopped it, killed it before it started... but where's the fun in that?"_

* * *

The spindly arm came up, those eyeless sockets locked onto her...

Dozens of smoke trails appeared in an instant before explosions ripped across the surface of the monster's sickly flesh. The creature stumbled backwards under the onslaught. The roar of engines filled the air and the pegasus turned her head skyward. Pie Industries Aerofighters, she'd seen them in a magazine but never in real life, never thought she would have the chance to.

Yet, there they were, shooting rockets at this monster, fighting it off, or trying to. A dull thrumming soon revealed itself overhead, some kind of military airship, she watched in stunned fascination as it opened fire on the behemoth. The logo emblazoned on the pure white hull was one she was unfamiliar with._ 'HERD?' _she thought to herself as it fired a second volley.

The monster let out a scream that seemed to penetrate into the deepest layers of the orange pony's mind as it's spindly arm came up again and a blast of energy fired from the palm of its hand. The sickly green energy lanced through the airship and exploded in the distance.

The pegasus was frozen in place as the airship began to lazily descend towards her, trailing fire and smoke as vital lift gas vented from the gaping hole in the envelope. The cannons kept firing even as it started to angle down towards her, still under power.

A new sound pierced her awareness, a loud raspy whine, rapidly approaching. She finally tore her gaze away from the falling airship, this new sound enough to break her trance. She locked eyes with a cyan pegasus atop a... _'What is that thing called?'_ she thought, the two wheeled machine stood, idling before her.

"Sorry I'm late, kid, hop on." The mare said to her, her voice betraying an intensity, an... almost smug quality, though her bearing conveyed that she just might be able to back it up. The orange pegasus shook the thoughts out of her head and awkwardly climbed onto the contraption behind the mare driving it.

"Just, put your forelegs around me and hold on." The cyan pegasus said from under he helmet a second before she twisted the throttle and the machine took off, leaving behind a thin black trail of rubber as the engine let out its raspy whine. She had a hard time holding onto the older mare as the acceleration and wind kept trying to push her off the back of the... _'Motorcycle, that's what it's called.'_ she thought with some satisfaction.

The orange pony chanced a look behind her and watched as the airship finally crashed into the ground, ponies of all color and size poured out of the crushed gondola as they abandoned the destroyed craft even as the engines burned. She let out a breath she hadn't been holding, she'd made it, and so had they.

"Scoots, give me a direct route to the cages, have the doctor meet us there. I've got the package, condition green. Storm is brewing." The driver of the motorcycle yelled from under her helmet as the bike surged forward in another burst of acceleration. "Whisper, right?" She yelled over her shoulder at the younger pony.

"Y-yes... Um... yes ma'am" she mumbled into the other pony's back, her eyes hidden under her red mane.

"Just like your mom then..." The rider muttered, "Name's Rainbow Dash, I'm sure your mother told you all about me and how awesome I am. She wasn't wrong!" She yelled back as the leaned the bike almost onto its side as she turned a corner and blasted through a wooden crossing gate.

Elsewhere, deep under the streets in an armored bunker, a figure picked up a phone. "She's on her way then? Good. Tell Vinyl to get Unit One ready for activation. Have Sunset on standby in case the spare proves useless." The cradle clacked as the receiver settled into it.

"Was it really necessary to be that harsh?"

"Let it be. Familiarity brings loss, I've lost enough already. Don't you have preparations to be making?" A long sigh, and an even longer pause. "When this is all over, if we still have any time left..."

"Alright, we're on it!" the white unicorn yelled before shutting off the intercom. She turned to face her assembled staff, "Alright, it's show time everypony, we're launching Unit One in five minutes, drain all coolant tanks, bring the entry plug online, and start unbolting the restraints. This is it!" she yelled out.

Behind the mare, dozens upon dozens of bolts unscrewed into the room from the holding cage beyond, bright pink coolant flowed through troughs under the steel grid flooring. The walls creaked and groaned as thousands of tons of pressure were slowly released.

Monitors lit up, the soft glow reflecting off her tinted glasses as telemetry and statistics filled up the displays in neatly ordered lists. She tapped a forehoof on her head in concentration as she studied a schematic display of Unit One.

"Lookin good... Now to go see if Sunset can be ready as a backup..." She muttered to herself as she pushed herself away from her desk. She let out a sigh as she stood up from her chair and turned to the door, "Okay Sunset, let's see how creepy you can be today..."

"Are we... lost?" Whisper asked softly as she followed Rainbow Dash down what must have been the fiftieth hallway since they had arrived.

Dash turned around, her slightly faded mane trailed behind her as she rotated in place. "What? No, of course we're not lost... This is just the scenic route" she said hastily as her eyes scanned the placards on the walls, trying to find out where she-

"Lost again huh?" a new voice asked.

"Applejack! I'm was just-" Dash started.

"Gettin lost again? C'mon, it's this way." Applejack started as she lead the other two in the _correct_ direction. She looked over at the younger pony, the one who was the same color as herself, if with a different mane, "Whisper? I ain't seen you in ages, didn't know you were the one they sent for..."

Dash eyed the young pony and then looked back to her old friend, _'There's a definite similarity here...'_ "Hey AJ, if you've met her before does that mean that-"

"Aunt Applejack, yes. No, I didn't think it would ever happen either. Yes, there's a reason I didn't tell you. Yes, this conversation is that reason." Applejack rapid-fired, interrupting Dash's question and cutting off future conversation on the topic in one fell swoop.

"Aunt?" Whisper asked hesitantly, "I don't really remember you..." She continued as she followed along, continuing to hide her face behind her mane. _'She looks kind of like the pictures though...'_ she thought in reflection.

"Oh... You weren't but a year old back then, still I'd recognize ya anywhere." Applejack explained as she slapped her hoof on a door release, "Didn't expect the new recruit to be you though..." she trailed off.

"It can't be us." Dash interjected, "Not now."

"Um... What am I here for, exactly?" Whisper asked, breaking into the exchange between the two older mares as they crossed the threshold into the darkened room beyond.

"You're here to pilot Evangelion. You're here to protect Equestria from the greatest threat it's ever known. You are here to serve" came her answer, the voice masculine, older, but not much. She turned her head up, she recognized the dragon. He was older than the picture, had grown more, but those colors, that he was a dragon, there was only one that he could be.

"S-spike?" she asked hesitantly, peeking out from under her mane with one eye.

"Correct." He said tersely. With a snap of his claw the lights came up and the room was bathed in illumination.

Whisper looked around the room as she blinked away her sudden flash blindness, and then she saw it. The massive purple armored face, staring at her, staring into her soul. She shivered as she felt a chill rush through her. "I... I can't..." she sputtered in fear. _'Pilot this? I've never seen anything like it before in my life, and they expect me to...'_

"Disappointing." He spat as he turned and pressed a claw to the intercom, "Send in Sunset, she'll have to do it again. This pilot is useless."

Whisper fell to her knees, her eyes locked onto the floor as she heard his words. _'So... they didn't need me anyway... I'm... I'm just useless...'_ she thought to herself as the tears pooled at her hooves. She could hear the other ponies on the catwalk moving around, but she couldn't hear what they were saying, her own quiet whimpering drowning them out.

A new noise pierced her consciousness, caster wheels rolling on metal grating. She looked up, blinked away her tears, and saw a hospital bed rolling out, being pushed by nurse-ponies. _'They can't be...'_ she thought incredulously.

An explosion shook the catwalk, the bed tipped, the purple pony laying on it started to fall... Whisper pumped her wings and kicked off of the catwalk. Crossing the distance in an instant, she caught the falling pony. She didn't look any older than herself, a lavender colored unicorn, heavily bandaged.

And bleeding, she noticed, as she stood there, holding the other pony in her forelegs. _'This is Sunset? This is the... she can't do this... she'll...'_ she thought with rising anger. The pony in her arms was bleeding, bandaged, whimpering in pain. The unicorn's un-bandaged eye opened and looked up at her, an almost pleading sadness radiated from her face.

Whisper took a deep breath and turned her head to look up at Spike, her eyes locked with his, her face twisted in anger and determination, "Spike! I'll do it, I'll pilot this thing... Just don't make her do it!"

_"Listen, kid, that was really brave of you, even if nopony else ever tells you this, you did a really good thing."_ Dash said quietly into the radio.

Whisper looked at the video screen on the wall of the plug. She was sitting in the control seat of the purple mecha, two clips in her mane, her hooves on the control plates. She nodded to the video feed. "I just... couldn't let her do this... being so hurt." she answered softly.

_"Alright, Whisper is it? I'm Vinyl Scratch, I'm going to be running you through a few start-up checks while we fill the plug. I need you to just sit there and relax as best you can alright?"_ A new, white unicorn asked. Whisper almost laughed, the electric blue mane and tinted glasses didn't exactly scream professionalism, and the tone of voice betrayed somepony who'd be more at home partying than working on giant robots.

_"Okay, looks like you've got a good neural link... we're going to fill the plug with LCL now, just breathe it in, you won't drown. I promise."_ Vinyl announced as a sticky orange liquid began to pour into the plug from all sides, rapidly filling it up to her neck... and then over her head completely.

Whisper held her breathe despite the assurances the unicorn had given her. She'd never liked swimming, and now they wanted her to breathe in this... stuff? She struggled for a few more seconds before finally giving in to her lungs demand to breathe.

_'It tastes like blood...'_ was her first stunned thought as she choked the fluid into her lungs. She expected to drown but the burning never came, in fact, it was the exact opposite, her lungs felt perfectly fine. Her stomach was twisting itself in knots, however. "I feel sick."

_"That'll pass. You're looking good Whisper, sync is... seventy eight percent. We can do this!"_ Vinyl yelled as she turned away from the camera.

_"Alright. This is it. Whisper, we'll get through this together, I promise. Eva launch!"_ Dash yelled and in an instant Whisper felt as though her head was going to get pushed through her torso as the acceleration slammed her down into the seat.

Moments later, after what felt like an eternity, the Eva stopped on its launch rails, Whisper looked through the view screens surrounding her and took in the sight of the streets of New Canterlot. The same streets she'd been on not even hours ago.

She felt the weight hit her shoulders as the locking clamps released, she felt... like she was wearing armor. _"Okay, Eva operates on your thoughts, you pilot with your mind. I want you to think about walking, just concentrate on walking right now okay?"_ Vinyl said through the radio, audio only.

Whisper nodded her head and then concentrated. The Eva took a single step foward out of the launch elevator. _'Just one hoof in front of the other...'_ she thought as she pushed the Eva forward. The monster was standing in front of her, eying her curiously.

She glanced at it and her concentration slipped. The Eva's front hoof caught on a street light and she tripped. Whisper held onto the controls tightly as the ground rushed up to meet her face. She hit, her own face hurt with the impact, she felt like she'd been knocked senseless as the ground started to shake.

She looked up to see the monster standing over her, saw its hand coming down, grabbing onto the Eva's face. She heard dash and Vinyl screaming over the radio, heard the alarm buzzers filling the cockpit. She was frozen in terror as the monster's palm lit up.

Crack. A spike shot out of the monster's palm and slammed into the face armor of the Eva. Crack, a second blow, the display was showing the cracks in the armor, she felt a pounding in her head. Crack, the spike shot through the armor and went completely through Eva's head.

Whisper screamed in pain, the monster kicked the Eva backwards into a building. Whisper's head slammed into the back of her seat and she blacked out. Red fluid started to pour from the wound in the mecha's head.

"Pulses are flowing backwards, Eva is rejecting the connection!" Yelled a young white unicorn.

"Massive damage to the cranial nerve cluster, we cannot maintain activation! Unit will be offline in eight seconds!" Yelled a yellow earth pony.

"Oh no... Shut down the A-10 connections, bring life support up to maximum. Applebloom, send the ejection signal and recover the pilot!" Vinyl yelled, as she stepped forward to an unoccupied console, her hooves dancing across the controls as she tried to do something, anything to recover the situation.

"Negative, it's rejecting the signal!" Applebloom yelled as she frantically tried to over-ride the built in safeties.

"What have we done..." Dash said under her breath as her eyes remained locked on the video feed, the disabled Eva still rested against the building.

"W-wait! I've got something!" The young white unicorn yelled, her eyes wide with shock.

"Sweetie Belle? what is it?" Vinyl yelled to her over the blaring of alarms.

"Eva is... it's reactivating!"


End file.
